There is a warning. IIRC it says "are you sure you want to discard all changes? This action is unreverisble". In the context of version management. Creating a file is a change. And just below the button to discard all changes is the list of changes. In that list he could've seen 3000 changes of the type "file creation", when you discard a file creation, it means to undo the creation, which is a deletion.

The button days what is going to do. There is a warning about what it's going to do. And there is a list of the exact changes it's going to undo.

The only way to avoid this from happening is to not have the button exist. In that case, the users that actually want to discard all changes would be unable to do so.